Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

Abstract

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FST rankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

“…Sampling site details, sample collection and preparation methods are described in Sinclair-Waters et al . 10,17 and Berg et al . 12 .…”

“…We combined Atlantic cod ( Gadus morhua ) genotype data from three studies conducted by Sinclair-Waters et al 10,17 and Berg et al . 12 (Supplementary Table 1).…”

“…Recent genomic analyses have revealed large chromosomal rearrangements on four linkage groups (LG1, LG2, LG7 and LG12) 10,12 . Two adjacent inversions within LG1 16 and the rearrangement on LG12 differentiate offshore migratory and coastal non-migratory populations 4, 10, 16, 17 . The migratory phenotype exhibited by Northern cod may have imposed increased vulnerability to overfishing in these populations.…”

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

“…Atlantic cod ( Gadus morhua ), a heavily exploited, demersal, broadcast spawning marine fish, provides a study system well suited to investigate the extent of modularity and parallelism among genomic architectural features. Atlantic cod exhibit high connectivity and dispersal, but also show divergent adaptation and genetic structuring associated with genomic architectural variation (Barth et al, ; Sinclair‐Waters, Bentzen, et al, ). Past genetic studies of Atlantic cod have suggested parallel environmental adaptation to temperature and salinity in the east and west Atlantic (Berg et al, ; Bradbury et al, ).…”

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

“…Individual and regional genomic structural diversity that differentiates Atlantic cod populations by environment and migratory behavior has been identified across the species range in the North Atlantic ( 10 ). Recent genomic analyses have revealed large chromosomal rearrangements on four linkage groups (LG1, LG2, LG7, and LG12) ( 7 , 10 ); two adjacent inversions within LG1 ( 14 ) have been shown to consistently differentiate offshore migratory and coastal nonmigratory populations ( 7 , 9 , 14 , 15 ). The migratory phenotype exhibited by Northern cod may have imposed increased vulnerability to overfishing in these populations ( 16 ).…”